Men1237-TableS5.txtplain text document, 171.8 KB Table S4 Plastid genome alignment used for phylogenetic analyses. Men1237-TableS4.txtplain text document, 5.3 MB Table S2 List of primer pairs used to amplify 11 nuclear single copy genes of New Caledonian Araucaria species. Men1237-TableS2.docxWord document, 13.7 KB Table S1 List of primer pairs used to amplify the plastid genome of New Caledonian Araucaria species (P101 to P158). Men1237-TableS1.docxWord document, 16.5 KB Men1237-FigureS3.pdfapplication/PDF, 516.5 KBįig. S3 Neighbor joining tree based on 11 nuclear genes. Men1237-FigureS2.pdfapplication/PDF, 21 KBįig. S2 Bayesian inference tree based on 11 nuclear genes. Men1237-FigureS1.pdfapplication/PDF, 518.5 KBįig. S1 Neighbor joining tree based on complete plastid sequences. The big challenge therefore remains to develop techniques that allow routine access to large numbers of nuclear markers scaleable to thousands of individuals from phylogenetically disparate sample sets.
Modest gains in discrimination thus are possible, but using complete plastid genomes or a small number of nuclear genes in DNA barcoding may not substantially raise species discriminatory power in many evolutionarily young lineages. However, the plastid data retrieved a phylogeny with a higher resolution compared to any previously published tree of this clade and supported the monophyly of about twice as many species and nodes compared to the nuclear data set. Overall, fewer than half of the New Caledonian Araucaria species with multiple accessions were monophyletic in the plastid or nuclear trees. Additionally, 11 nuclear gene regions were Sanger sequenced for all accessions to ascertain the success of species discrimination using a moderate number of nuclear genes. We have tested the power of complete plastid genomes to discriminate among multiple accessions of 11 of 13 New Caledonian Araucaria species, an evolutionarily young lineage where the standard DNA barcoding approach has so far failed and phylogenetic relationships have remained elusive. The usefulness of this approach, however, depends on the extent to which plastid haplotypes track morphological species boundaries.
Complete plastid genome sequencing offers an increasingly easy-to-access source of characters that helps address this. Obtaining accurate phylogenies and effective species discrimination using a small standardized set of plastid genes is challenging in evolutionarily young lineages.